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On 1/12/2010 2:29 PM, 铁锋 彭 wrote:
<blockquote cite="mid:567393.99682.qm@web15605.mail.cnb.yahoo.com"
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<td style="font: inherit;" valign="top">Hi everyone,<br>
<br>
I first created 3 x 3 x 3 nm water, 895 water using
genbox. Then i used<br>
<br>
editconf -bt triclinic -f tension.gro -o conf.gro -c
-box 3 3 9 -angles 90 90 90<br>
<br>
make the water in x=y=3, z=9 nm box.<br>
<br>
Then <br>
grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -po
mdout2.mdp -maxwarn 10<br>
<br>
mdrun -v -s em -e pr -o pr -c after_pr<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 5.00000e+01<br>
Number of steps = 100000<br>
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.26219e+04 Fmax=
1.42837e+04, atom= 379<br>
Step= 1, Dmax= 1.0e-02 nm, Epot= -2.54567e+04 Fmax=
5.60900e+03, atom= 1870<br>
Step= 2, Dmax= 1.2e-02 nm, Epot= -2.83385e+04 Fmax=
2.94370e+03, atom= 283<br>
Step= 3, Dmax= 1.4e-02 nm, Epot= -3.05598e+04 Fmax=
1.45800e+03, atom= 2077<br>
Step= 4, Dmax= 1.7e-02 nm, Epot= -3.28940e+04 Fmax=
9.07848e+02, atom= 1726<br>
Step= 5, Dmax= 2.1e-02 nm, Epot= -3.49312e+04 Fmax=
1.90443e+03, atom= 1726<br>
Step= 6, Dmax= 2.5e-02 nm, Epot= -3.55885e+04 Fmax=
1.64255e+03, atom= 1726<br>
Step= 7, Dmax= 3.0e-02 nm, Epot= -3.62927e+04 Fmax=
1.83479e+03, atom= 1726<br>
Step= 8, Dmax= 3.6e-02 nm, Epot= -3.68613e+04 Fmax=
2.20746e+03, atom= 1726<br>
Step= 9, Dmax= 4.3e-02 nm, Epot= -3.73153e+04 Fmax=
2.09106e+03, atom= 1726<br>
<br>
t = 0.010 ps: Water molecule starting at atom 1726 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
Step= 10, Dmax= 5.2e-02 nm, Epot= -3.77143e+04 Fmax=
7.92103e+04, atom= 1727<br>
Step= 26, Dmax= 1.9e-06 nm, Epot= -3.25046e+04 Fmax=
2.08556e+05, atom= 1930<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 50<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or
turn<br>
off constraints alltogether (set constraints = none in mdp
file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in 27
steps,<br>
but did not reach the requested Fmax < 50.<br>
Potential Energy = -3.7714320e+04<br>
Maximum force = 7.9210281e+04 on atom 1727<br>
Norm of force = 2.0394656e+03<br>
<br>
grompp -f grompp.mdp -c after_pr.gro -p topol.top -o
run.tpr -po mdout3.mdp -maxwarn 10<br>
<br>
<br>
<br>
uqtpeng1@ce102-0419:~/water/surfacetension/339$ mdrun -v
-s run -e pr2 -o pr2 -c after_pr2 -g prlog >&
pr.job &<br>
Program mdrun, VERSION 4.0.7<br>
Source code file: ../../../../src/mdlib/nsgrid.c, line:
348<br>
<br>
Fatal error:<br>
Number of grid cells is zero. Probably the system and box
collapsed.<br>
<br>
So my problem is whether my EM result is good?<br>
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<br>
No, it isn't. There's at least one bad water molecule, like the
output said.<br>
<br>
<blockquote cite="mid:567393.99682.qm@web15605.mail.cnb.yahoo.com"
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<td style="font: inherit;" valign="top"><br>
and why the Number of grid cells is zero??<br>
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<br>
Because the system imploded.<br>
<br>
Mark<br>
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